LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-312-gf3113317cc-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread.
  using 1 OpenMP thread(s) per MPI task
## srp_react example script
## Author: Vaibhav Palkar
##
## Simulates controlled degradation of a nanogel particle
## in a simulation box and prints statistics regarding
## the fraction of bonds broken over time.

variable       rseeddpd  equal  26817
variable       rseedvel  equal  5991
variable       breakstep equal  10
variable       probbreak  equal 0.0009
variable       rseedbreak equal 6777

# simulation time
#***********************************************
variable       mainsteps     equal  10000

# simulation setup
#***********************************************
units          lj
atom_style     molecular
boundary       p  p  p
bond_style     harmonic
#lattice        fcc   3.0
comm_modify    cutoff 4.0 vel yes

# initial nanogel
#***********************************************
read_data   gel_equil.dat
Reading data file ...
  orthogonal box = (0 0 0) to (15 15 15)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  11017 atoms
  reading velocities ...
  11017 velocities
  scanning bonds ...
  4 = max bonds/atom
  orthogonal box = (0 0 0) to (15 15 15)
  1 by 2 by 2 MPI processor grid
  reading bonds ...
  892 bonds
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     4 = max # of 1-3 neighbors
     8 = max # of 1-4 neighbors
    12 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.031 seconds

# define groups, create solvent atoms
#**************************************************
group          Npoly         type   1 2 3 4
858 atoms in group Npoly
group          water         type   5
9267 atoms in group water
group          N_all         type   1 2 3 4 5
10125 atoms in group N_all

# density check
#***********************************************
variable       N_atoms  equal  count(all)
variable       tdens equal count(all)/vol
print          "The system density is now ${tdens}"
The system density is now 3.2642962962963

# bond break settings
# #***********************************************
fix            break  N_all     bond/break  ${breakstep}   2   0  prob   ${probbreak}    ${rseedbreak}
fix            break  N_all     bond/break  10   2   0  prob   ${probbreak}    ${rseedbreak}
fix            break  N_all     bond/break  10   2   0  prob   0.0009    ${rseedbreak}
fix            break  N_all     bond/break  10   2   0  prob   0.0009    6777

# interaction parameter setting
#***********************************************
mass             *   1.0
bond_coeff       *   500.0   0.70
special_bonds  lj   1  1  1
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    1        1        1       
  special bond factors coul:  0        0        0       
     4 = max # of 1-2 neighbors
     4 = max # of 1-3 neighbors
     8 = max # of 1-4 neighbors
    12 = max # of special neighbors
  special bonds CPU = 0.000 seconds
newton         on

pair_style     hybrid dpd  1.0  1.0  ${rseeddpd} srp/react 0.8 * mid break
pair_style     hybrid dpd  1.0  1.0  26817 srp/react 0.8 * mid break
#***********************************************
pair_coeff     *5     *5   dpd   78.000    4.5   1.0
pair_coeff     *4      5   dpd   79.500    4.5   1.0
pair_coeff     *5      6   none
pair_coeff      6      6   srp/react   80.00 0.800

# initial velocity
#***********************************************
velocity       all create 1.0 ${rseedvel} dist gaussian mom yes
velocity       all create 1.0 5991 dist gaussian mom yes

# integrator control
#***********************************************
neighbor       0.3 bin
neigh_modify   every 1 delay 5 check  no
timestep       0.02

# Access variables of fix bond/break
#**********************************************
variable      Nbreak    equal  f_break[2]   # Number of bonds broken
variable      TIME      equal  time

# ensemble setting
#***********************************************
fix            1  all  nve

# print bonds breaking stats
# ***********************************************
variable TotBreak equal 100 # total breakable bonds in current system
#fix print_bonds_broken all print 100 "${TIME} ${Nbreak} $((v_TotBreak-v_Nbreak)/v_TotBreak)" file bonds_broken.txt screen no title "time bonds_broken fraction_bonds_intact"

# thermo output
#***********************************************
thermo         100
thermo_style   custom step temp pe ke etotal epair
thermo_modify  norm  no

reset_timestep 0
#dump          1 Npoly   custom 5000 traj.lammpstrj id type x y z
#*********************************************
run           ${mainsteps}
run           10000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- pair srp command: doi:10.1063/1.3698476

@Article{Sirk2012
 author = {T. W. Sirk and Y. R. Sliozberg and J. K. Brennan and M. Lisal and J. W. Andzelm},
 title = {An Enhanced Entangled Polymer Model for Dissipative Particle Dynamics},
 journal = {J.~Chem.\ Phys.},
 year =    2012,
 volume =  136,
 pages =   {134903}
}

- pair srp/react style: doi:10.1021/acs.jpcb.1c09570

@Article{palkar2022
 author = {Palkar, Vaibhav and Kuksenok, Olga},
 title = {Controlling Degradation and Erosion of Polymer Networks: Insights from Mesoscale Modeling},
 journal = {J.~Phys.\ Chem.~B},
 year = 2022,
 volume = 126,
 number = 1,
 pages = {336--346}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Using type 6 for bond particles
Thermo normalization turned off by pair srp/react
Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 5 steps, check = no
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.3
  ghost atom cutoff = 4
  binsize = 0.65, bins = 24 24 24
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair dpd, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair srp/react, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Removed/inserted 892/892 bond particles.
Per MPI rank memory allocation (min/avg/max) = 16.21 | 16.24 | 16.33 Mbytes
   Step          Temp          PotEng         KinEng         TotEng         E_pair    
         0   1.0009302      127698.37      15200.126      142898.49      127171.17    
Removed/inserted 892/891 bond particles.
       100   1.0113664      127760.53      15358.61       143119.14      127196.9     
Removed/inserted 891/890 bond particles.
       200   1.0233698      127619.25      15540.894      143160.14      127068.35    
Removed/inserted 890/889 bond particles.
       300   1.0151246      127663.32      15415.683      143079         127127.54    
       400   1.0141165      127701.19      15400.374      143101.56      127136.2     
       500   1.0129614      127774.16      15382.831      143156.99      127219.51    
Removed/inserted 889/888 bond particles.
       600   1.0059207      127614.61      15275.911      142890.52      127060.76    
       700   1.0121763      127555.63      15370.91       142926.54      127054.21    
Removed/inserted 888/887 bond particles.
       800   1.0117644      127671.13      15364.654      143035.78      127098.99    
Removed/inserted 887/886 bond particles.
       900   1.0165272      127573.58      15436.982      143010.57      127015.57    
Removed/inserted 886/885 bond particles.
      1000   1.0080102      127866.72      15307.643      143174.37      127287.85    
      1100   1.0061798      127916.1       15279.847      143195.94      127331.89    
Removed/inserted 885/884 bond particles.
Removed/inserted 884/883 bond particles.
      1200   1.0102919      127743.97      15342.293      143086.26      127145.63    
      1300   1.0065585      127544.3       15285.598      142829.9       126980.91    
      1400   0.98981907     127755.19      15031.392      142786.59      127192.98    
      1500   1.0099047      127523.33      15336.413      142859.74      127006.58    
Removed/inserted 883/882 bond particles.
Removed/inserted 882/881 bond particles.
      1600   1.0074967      127619.6       15299.844      142919.44      127063.78    
Removed/inserted 881/879 bond particles.
      1700   1.0170579      127685.46      15445.041      143130.5       127177.58    
      1800   1.0298028      127663.51      15638.585      143302.1       127118.76    
Removed/inserted 879/878 bond particles.
      1900   1.0040143      127647.36      15246.961      142894.32      127124.53    
Removed/inserted 878/877 bond particles.
      2000   1.0127655      127864.06      15379.857      143243.92      127282.66    
      2100   1.0238539      127683.9       15548.245      143232.15      127134.34    
      2200   1.0018755      127720.45      15214.481      142934.93      127140.84    
Removed/inserted 877/876 bond particles.
Removed/inserted 876/875 bond particles.
Removed/inserted 875/874 bond particles.
      2300   1.0118697      127574.85      15366.254      142941.1       127055.34    
      2400   1.0104868      127822.16      15345.253      143167.42      127266.22    
Removed/inserted 874/873 bond particles.
      2500   1.0252753      127578.82      15569.83       143148.65      127032.95    
Removed/inserted 873/872 bond particles.
      2600   0.99322615     127651.6       15083.132      142734.73      127133.55    
      2700   1.0279646      127669.25      15610.67       143279.92      127055.87    
Removed/inserted 872/871 bond particles.
Removed/inserted 871/870 bond particles.
      2800   1.0136938      127798.85      15393.954      143192.8       127263.88    
Removed/inserted 870/869 bond particles.
      2900   1.0126037      127628.77      15377.401      143006.18      127073.21    
Removed/inserted 869/868 bond particles.
      3000   1.0093218      127794.71      15327.562      143122.27      127247.35    
Removed/inserted 868/867 bond particles.
Removed/inserted 867/866 bond particles.
      3100   1.0120427      127563.79      15368.88       142932.67      127020.98    
Removed/inserted 866/865 bond particles.
Removed/inserted 865/864 bond particles.
      3200   1.0264764      127806.78      15588.071      143394.85      127236.01    
      3300   1.0117158      127812.21      15363.916      143176.13      127258.61    
Removed/inserted 864/863 bond particles.
      3400   1.0136065      127648.94      15392.629      143041.57      127129.58    
Removed/inserted 863/862 bond particles.
Removed/inserted 862/861 bond particles.
      3500   1.0120233      127556.28      15368.586      142924.87      126998.33    
      3600   1.0140105      127408.18      15398.764      142806.94      126843.86    
      3700   1.0187266      127660.25      15470.382      143130.63      127110.87    
Removed/inserted 861/860 bond particles.
      3800   1.0127633      127686.18      15379.823      143066.01      127141.77    
      3900   1.0133219      127502.75      15388.307      142891.05      126977.58    
      4000   1.0023014      127640.36      15220.95       142861.31      127173.77    
Removed/inserted 860/859 bond particles.
      4100   1.0049282      127530.96      15260.84       142791.8       126994.11    
      4200   1.0055188      127418.54      15269.808      142688.34      126884.86    
Removed/inserted 859/858 bond particles.
Removed/inserted 858/857 bond particles.
Removed/inserted 857/856 bond particles.
      4300   0.99110226     127758.61      15050.879      142809.49      127224.1     
      4400   1.016243       127743.41      15432.666      143176.08      127208.66    
      4500   1.0272015      127556.76      15599.082      143155.84      127021.5     
      4600   1.0213958      127637.33      15510.917      143148.24      127095       
      4700   1.0182032      127785.14      15462.434      143247.57      127234.59    
      4800   1.0154088      127587.19      15419.997      143007.19      127047.99    
      4900   0.99999138     127391.26      15185.869      142577.13      126867.83    
      5000   0.99542038     127640.67      15116.454      142757.13      127106.98    
      5100   1.0087213      127602.92      15318.442      142921.36      127012.59    
Removed/inserted 856/855 bond particles.
      5200   1.0152818      127578.56      15418.069      142996.63      127059.55    
      5300   1.0142815      127739.61      15402.88       143142.49      127179.28    
      5400   0.99963473     127767.59      15180.453      142948.04      127241.17    
      5500   1.0070496      127518.58      15293.056      142811.64      127037.85    
      5600   1.0106221      127750.93      15347.308      143098.24      127156.79    
Removed/inserted 855/854 bond particles.
      5700   1.0126347      127634.96      15377.87       143012.83      127097.55    
      5800   1.0189337      127575.45      15473.528      143048.97      127034.05    
      5900   1.0002092      127534.98      15189.177      142724.15      127002.78    
      6000   1.0087639      127648.78      15319.089      142967.87      127114.06    
Removed/inserted 854/853 bond particles.
      6100   1.0060471      127627.46      15277.831      142905.29      127051.85    
      6200   1.0226411      127580.45      15529.828      143110.27      127059.17    
      6300   1.017129       127727.68      15446.122      143173.81      127197.39    
Removed/inserted 853/852 bond particles.
      6400   1.021953       127615.91      15519.379      143135.28      127080.8     
      6500   1.0019976      127688.81      15216.336      142905.14      127183.87    
      6600   1.013033       127689.78      15383.92       143073.7       127136.19    
Removed/inserted 852/851 bond particles.
      6700   1.0136212      127786.33      15392.851      143179.18      127242.02    
Removed/inserted 851/850 bond particles.
      6800   1.0164571      127716.53      15435.917      143152.45      127216.89    
Removed/inserted 850/849 bond particles.
      6900   0.99885902     127553.21      15168.673      142721.89      127035.24    
      7000   0.99135435     127688.74      15054.707      142743.44      127129.09    
Removed/inserted 849/847 bond particles.
      7100   1.008181       127588.87      15310.236      142899.11      127101.33    
      7200   0.99459456     127456.95      15103.913      142560.86      126926.41    
      7300   1.006134       127699.43      15279.151      142978.58      127172.36    
      7400   1.0189526      127444.52      15473.814      142918.34      126931.71    
      7500   1.0071328      127745.36      15294.319      143039.68      127195.43    
      7600   1.0150051      127520.52      15413.868      142934.39      126990.34    
Removed/inserted 847/846 bond particles.
      7700   1.0110038      127613.52      15353.104      142966.63      127064.25    
      7800   1.0096271      127622.02      15332.197      142954.22      127060.38    
      7900   0.99629754     127766.65      15129.774      142896.43      127260.11    
Removed/inserted 846/845 bond particles.
Removed/inserted 845/844 bond particles.
      8000   1.0095004      127614.66      15330.273      142944.94      127097.17    
      8100   1.0074855      127710.72      15299.675      143010.4       127186.61    
      8200   1.0182298      127572.35      15462.838      143035.19      127042.67    
      8300   1.0079071      127844.95      15306.078      143151.03      127317.29    
Removed/inserted 844/843 bond particles.
      8400   1.0102345      127774.33      15341.421      143115.76      127255.71    
      8500   1.0058972      127664.15      15275.554      142939.7       127157.33    
      8600   1.0164353      127544.99      15435.586      142980.58      127032.86    
      8700   1.0079305      127688.46      15306.433      142994.9       127156.4     
      8800   1.0156761      127665.12      15424.058      143089.18      127158.6     
      8900   1.0120501      127702.23      15368.994      143071.23      127135.39    
Removed/inserted 843/842 bond particles.
Removed/inserted 842/841 bond particles.
      9000   1.0238751      127719.23      15548.567      143267.8       127203.41    
Removed/inserted 841/840 bond particles.
      9100   1.0244878      127735.47      15557.871      143293.35      127229.4     
      9200   1.020667       127619.92      15499.849      143119.77      127066.15    
      9300   1.002636       127818.34      15226.03       143044.37      127253.68    
      9400   1.0092543      127824.19      15326.536      143150.73      127269.3     
Removed/inserted 840/839 bond particles.
Removed/inserted 839/838 bond particles.
      9500   1.0043769      127609.35      15252.467      142861.82      127062.74    
Removed/inserted 838/837 bond particles.
      9600   0.99776107     127487.58      15152          142639.58      126972.51    
      9700   1.0156158      127570.93      15423.142      142994.07      127055.7     
      9800   1.0212284      127772.7       15508.374      143281.08      127225.13    
      9900   1.0116191      127793.08      15362.448      143155.53      127288.94    
Removed/inserted 837/836 bond particles.
     10000   1.0129247      127582.88      15382.274      142965.16      127098.63    
Deleted 836 atoms, new total = 10125
Loop time of 15.5803 on 4 procs for 10000 steps with 10125 atoms

Performance: 1109095.988 tau/day, 641.838 timesteps/s, 6.499 Matom-step/s
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 7.3039     | 7.4554     | 7.5618     |   3.9 | 47.85
Bond    | 0.011791   | 0.017178   | 0.023545   |   3.8 |  0.11
Neigh   | 4.5206     | 4.5277     | 4.5382     |   0.3 | 29.06
Comm    | 2.4959     | 2.6124     | 2.7831     |   7.5 | 16.77
Output  | 0.0021423  | 0.0024499  | 0.0030088  |   0.7 |  0.02
Modify  | 0.80662    | 0.81987    | 0.83205    |   1.2 |  5.26
Other   |            | 0.1453     |            |       |  0.93

Nlocal:        2531.25 ave        2555 max        2515 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Nghost:          14082 ave       14107 max       14060 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Neighs:              0 ave           0 max           0 min
Histogram: 4 0 0 0 0 0 0 0 0 0

Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0.5997037
Neighbor list builds = 2054
Dangerous builds not checked
#***********************************************
Total wall time: 0:00:15
